Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaatggtttacgttatgggcatttttggtataggtattgccctgttcaaattttcctaggttttttagacatggtaagttga...

Basic information

species Zea mays
transcript GRMZM5G871262_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 4
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagttt-attttaaacttaatggtttacgttatgggcatttttggtataggtattgccctgttcaaattttcctaggttttttagacatggtaagttga----
 |||||||| |||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||| |||| || ||||||||||| || ||||| |||||||| | || || ||| ||| ||| | ||||   | ||| || ||||| ||     || ||||   | | || |  |   |      | ||  || |    
CACTGCACCTGCTAACTCTCAAACAACTTGGACAATGCGCGCTACCTTCCCTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACAgtgagttttacttcaatcttcatgttttgctttatcaccgtttctg-tatagctaca--tctattca--ctctactggtctgcatgtgaccgatagctttatgtc

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G19230.1 (Glycine max), 5'ss of exon 3
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTG-GTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaatggtttacgttatgggcatttttggtataggtattgccctgttcaaattttcctaggttttttag---acatggtaagttga
  ||||     ||   ||  | | ||| ||||| |||||| ||||||| || ||||||||  ||||| ||| |||| ||||||||||||||||||||  | || || | ||| |  |   |||   |||  |||   |  |   |  |   | |  |    ||    |  |||    | || ||| |   ||||  |   ||  
-TCTGCTAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTTGTTGCACTTGCTACTATTGTTGGATCTGTGCTTTTTGCTgtaagctcattcttcataaaat---ttaatttacctgtttcaattttcctgcttcttatttggcataggtttttaggcttgtttggttaacattattgttttg

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 4
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaatg--gtttacgttatgggcatttttggtataggtattgccctgttcaaattttcctaggttttt-tagacatggtaagttga
 |||||     ||   ||  | | ||| ||||| |||||| ||||||| || |||||||| ||||||||| | || ||||||||||||||||||||  | || |||| ||  || |    |||  |  || ||  |       ||   |||  ||| | |  | ||  ||||||| |   ||||  | |  |  ||  ||   
CACTGCCAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTGTTGCTCTTGCCACTATTGTTGGATCTGTGCTTTTTGCTgtaagttaatcgtatatcgtatgctgcctaggtagtttatgggtt---tatctgtactactttctttcaattttcattttttttccttgtgaaagtgtgtgtg

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 4
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaatggtttacgttatgggcatttttgg---tataggtattgccctgttcaaattttcctaggttttttagacatggtaagttga
 |||||     ||   ||  ||| ||| ||||| |||||| ||||||| ||||||||||| ||||||||| | || ||||||||||||||||||||  | || |||| ||  || |    ||| |      || ||   ||| |||   |||   || | |  | ||  |||| || |   |||| | |  |  ||  ||   
CACTGCCAGTCCTTCATCAGAAAAAACATGGACCATGCGTACTACCTTTCCTGAATATGTCGTTGCTCTTGCCACTATTGTTGGATCTGTGCTTTTTGCTgtaagttaatcctatatcgtatgctgc---ctagggtagtttatggatttatctctactactttctttcaattatcattttttttcttgtgaaagtgtgtgtg

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G18160.1 (Glycine max), 5'ss of exon 4
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaatggtttacgttatgggcatttttggtataggtattgccctgttcaaattttcctaggttttttag----acatggtaagttga
  ||||     ||   ||  | | ||| ||||| |||||| ||||||| || |||||||| ||||| ||| |||| ||||||||||||||||||||  | || || | ||| |   | |||   || |  | |  |      ||    |   | ||     |   |  ||||  |||| || || |    ||||  |   ||  
CTCTGCTAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTGTTGCACTTGCTACTATTGTTGGATCTGTGCTTTTTGCTgtaagctcattct--tcataaaatttaatttaactgtttcaattttcctgcttcttatttggcataggtttt--taggcttgtttggttaacattattgttttt

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G43020.1 (Glycine max), 5'ss of exon 4
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaat--ggtttacgt-tatgggcatttttggtataggtattgccctgttcaaattttcctaggttttttagacatggtaagttga
  ||||     ||   ||  | | ||| ||||| |||||| ||||||| || |||||||| ||||| ||| |||||||||||||||||||||||||| | || || | ||| |  |   |||    || || | | |     ||  || |  |  | | ||   | |    |||      ||||  |  ||||  |   ||  
CTCTGCTAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTGTTGCACTTGCTACAATTGTTGGATCTGTGCTTTTCGCTgtaagctcattcttcataaaatttaattcacctgtttcaattttcctgcttcatatttggcataggtt---tttagacttgtttggttaacattattgttttg

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 5'ss of exon 4
TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttattttaaacttaatggtttacgttatgggcatttttggtataggtattgccctgttcaaattttcctaggttttttagac-atggtaagttga
||| ||     | |  ||  | | ||| ||||| |||||| |||| || || |||||||| ||||||||| | ||||||||||| || || |||||||||||  |   ||| |    || ||| |      |       ||  |   | |||  ||   ||||   |  ||    |   ||  | ||| |    ||  |  
TACAGCTAATCCCACATCTGAGAAAACATGGACTATGCGTACTACTTTTCCAGAATATGTTGTTGCTCTTGCGACAATTGTTGGGTCAGTTCTTTTCACGgtatgaccattgttc-tttcatgttgagaagtgcattgtttgctttgaaaggatttaatctgtcttatattgttgattcttcattgactaacacaaactct

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 306

TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttat ... tttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 257

TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttat ... tttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 269

TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttat ... tttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 355

TACTGCACCGGCTAACTCGCAAACAACTTGGACAATGCGTGCTACCTTCCCTGAATATGTGGTTGCTCTTACTACAATTGTTGGATCTGTGCTTTTCACGgtgagtttat ... tttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG